Peter V Kharchenko, Lev Silberstein, David T Scadden. Nat Methods 2014
Times Cited: 529
Times Cited: 529
Times Cited
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Integrating single-cell transcriptomic data across different conditions, technologies, and species.
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
Andrew Butler, Paul Hoffman, Peter Smibert, Efthymia Papalexi, Rahul Satija. Nat Biotechnol 2018
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The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn. Nat Biotechnol 2014
Cole Trapnell, Davide Cacchiarelli, Jonna Grimsby, Prapti Pokharel, Shuqiang Li, Michael Morse, Niall J Lennon, Kenneth J Livak, Tarjei S Mikkelsen, John L Rinn. Nat Biotechnol 2014
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Massively parallel digital transcriptional profiling of single cells.
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
Grace X Y Zheng, Jessica M Terry, Phillip Belgrader, Paul Ryvkin, Zachary W Bent, Ryan Wilson, Solongo B Ziraldo, Tobias D Wheeler, Geoff P McDermott, Junjie Zhu,[...]. Nat Commun 2017
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MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
Greg Finak, Andrew McDavid, Masanao Yajima, Jingyuan Deng, Vivian Gersuk, Alex K Shalek, Chloe K Slichter, Hannah W Miller, M Juliana McElrath, Martin Prlic,[...]. Genome Biol 2015
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
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Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
Evan Z Macosko, Anindita Basu, Rahul Satija, James Nemesh, Karthik Shekhar, Melissa Goldman, Itay Tirosh, Allison R Bialas, Nolan Kamitaki, Emily M Martersteck,[...]. Cell 2015
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Recovering Gene Interactions from Single-Cell Data Using Data Diffusion.
David van Dijk, Roshan Sharma, Juozas Nainys, Kristina Yim, Pooja Kathail, Ambrose J Carr, Cassandra Burdziak, Kevin R Moon, Christine L Chaffer, Diwakar Pattabiraman,[...]. Cell 2018
David van Dijk, Roshan Sharma, Juozas Nainys, Kristina Yim, Pooja Kathail, Ambrose J Carr, Cassandra Burdziak, Kevin R Moon, Christine L Chaffer, Diwakar Pattabiraman,[...]. Cell 2018
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Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
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Comparative Analysis of Single-Cell RNA Sequencing Methods.
Christoph Ziegenhain, Beate Vieth, Swati Parekh, Björn Reinius, Amy Guillaumet-Adkins, Martha Smets, Heinrich Leonhardt, Holger Heyn, Ines Hellmann, Wolfgang Enard. Mol Cell 2017
Christoph Ziegenhain, Beate Vieth, Swati Parekh, Björn Reinius, Amy Guillaumet-Adkins, Martha Smets, Heinrich Leonhardt, Holger Heyn, Ines Hellmann, Wolfgang Enard. Mol Cell 2017
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An accurate and robust imputation method scImpute for single-cell RNA-seq data.
Wei Vivian Li, Jingyi Jessica Li. Nat Commun 2018
Wei Vivian Li, Jingyi Jessica Li. Nat Commun 2018
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A general and flexible method for signal extraction from single-cell RNA-seq data.
Davide Risso, Fanny Perraudeau, Svetlana Gribkova, Sandrine Dudoit, Jean-Philippe Vert. Nat Commun 2018
Davide Risso, Fanny Perraudeau, Svetlana Gribkova, Sandrine Dudoit, Jean-Philippe Vert. Nat Commun 2018
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SAVER: gene expression recovery for single-cell RNA sequencing.
Mo Huang, Jingshu Wang, Eduardo Torre, Hannah Dueck, Sydney Shaffer, Roberto Bonasio, John I Murray, Arjun Raj, Mingyao Li, Nancy R Zhang. Nat Methods 2018
Mo Huang, Jingshu Wang, Eduardo Torre, Hannah Dueck, Sydney Shaffer, Roberto Bonasio, John I Murray, Arjun Raj, Mingyao Li, Nancy R Zhang. Nat Methods 2018
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ZIFA: Dimensionality reduction for zero-inflated single-cell gene expression analysis.
Emma Pierson, Christopher Yau. Genome Biol 2015
Emma Pierson, Christopher Yau. Genome Biol 2015
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SC3: consensus clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Kristina Kirschner, Michael T Schaub, Tallulah Andrews, Andrew Yiu, Tamir Chandra, Kedar N Natarajan, Wolf Reik, Mauricio Barahona, Anthony R Green,[...]. Nat Methods 2017
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A comparison of single-cell trajectory inference methods.
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
Wouter Saelens, Robrecht Cannoodt, Helena Todorov, Yvan Saeys. Nat Biotechnol 2019
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Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.
Aaron T L Lun, Karsten Bach, John C Marioni. Genome Biol 2016
Aaron T L Lun, Karsten Bach, John C Marioni. Genome Biol 2016
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Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors.
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
Laleh Haghverdi, Aaron T L Lun, Michael D Morgan, John C Marioni. Nat Biotechnol 2018
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Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells.
Allon M Klein, Linas Mazutis, Ilke Akartuna, Naren Tallapragada, Adrian Veres, Victor Li, Leonid Peshkin, David A Weitz, Marc W Kirschner. Cell 2015
Allon M Klein, Linas Mazutis, Ilke Akartuna, Naren Tallapragada, Adrian Veres, Victor Li, Leonid Peshkin, David A Weitz, Marc W Kirschner. Cell 2015
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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
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Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq.
Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz,[...]. Science 2015
Amit Zeisel, Ana B Muñoz-Manchado, Simone Codeluppi, Peter Lönnerberg, Gioele La Manno, Anna Juréus, Sueli Marques, Hermany Munguba, Liqun He, Christer Betsholtz,[...]. Science 2015
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Bias, robustness and scalability in single-cell differential expression analysis.
Charlotte Soneson, Mark D Robinson. Nat Methods 2018
Charlotte Soneson, Mark D Robinson. Nat Methods 2018
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Missing data and technical variability in single-cell RNA-sequencing experiments.
Stephanie C Hicks, F William Townes, Mingxiang Teng, Rafael A Irizarry. Biostatistics 2018
Stephanie C Hicks, F William Townes, Mingxiang Teng, Rafael A Irizarry. Biostatistics 2018
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Deep generative modeling for single-cell transcriptomics.
Romain Lopez, Jeffrey Regier, Michael B Cole, Michael I Jordan, Nir Yosef. Nat Methods 2018
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Current best practices in single-cell RNA-seq analysis: a tutorial.
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
Malte D Luecken, Fabian J Theis. Mol Syst Biol 2019
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mRNA-Seq whole-transcriptome analysis of a single cell.
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Normalizing single-cell RNA sequencing data: challenges and opportunities.
Catalina A Vallejos, Davide Risso, Antonio Scialdone, Sandrine Dudoit, John C Marioni. Nat Methods 2017
Catalina A Vallejos, Davide Risso, Antonio Scialdone, Sandrine Dudoit, John C Marioni. Nat Methods 2017
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Challenges in unsupervised clustering of single-cell RNA-seq data.
Vladimir Yu Kiselev, Tallulah S Andrews, Martin Hemberg. Nat Rev Genet 2019
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RNA velocity of single cells.
Gioele La Manno, Ruslan Soldatov, Amit Zeisel, Emelie Braun, Hannah Hochgerner, Viktor Petukhov, Katja Lidschreiber, Maria E Kastriti, Peter Lönnerberg, Alessandro Furlan,[...]. Nature 2018
Gioele La Manno, Ruslan Soldatov, Amit Zeisel, Emelie Braun, Hannah Hochgerner, Viktor Petukhov, Katja Lidschreiber, Maria E Kastriti, Peter Lönnerberg, Alessandro Furlan,[...]. Nature 2018
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Computational and analytical challenges in single-cell transcriptomics.
Oliver Stegle, Sarah A Teichmann, John C Marioni. Nat Rev Genet 2015
Oliver Stegle, Sarah A Teichmann, John C Marioni. Nat Rev Genet 2015
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Reversed graph embedding resolves complex single-cell trajectories.
Xiaojie Qiu, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah A Pliner, Cole Trapnell. Nat Methods 2017
Xiaojie Qiu, Qi Mao, Ying Tang, Li Wang, Raghav Chawla, Hannah A Pliner, Cole Trapnell. Nat Methods 2017
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SCANPY: large-scale single-cell gene expression data analysis.
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
F Alexander Wolf, Philipp Angerer, Fabian J Theis. Genome Biol 2018
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SCENIC: single-cell regulatory network inference and clustering.
Sara Aibar, Carmen Bravo González-Blas, Thomas Moerman, Vân Anh Huynh-Thu, Hana Imrichova, Gert Hulselmans, Florian Rambow, Jean-Christophe Marine, Pierre Geurts, Jan Aerts,[...]. Nat Methods 2017
Sara Aibar, Carmen Bravo González-Blas, Thomas Moerman, Vân Anh Huynh-Thu, Hana Imrichova, Gert Hulselmans, Florian Rambow, Jean-Christophe Marine, Pierre Geurts, Jan Aerts,[...]. Nat Methods 2017
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Accounting for technical noise in single-cell RNA-seq experiments.
Philip Brennecke, Simon Anders, Jong Kyoung Kim, Aleksandra A Kołodziejczyk, Xiuwei Zhang, Valentina Proserpio, Bianka Baying, Vladimir Benes, Sarah A Teichmann, John C Marioni,[...]. Nat Methods 2013
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Single-cell RNA-seq denoising using a deep count autoencoder.
Gökcen Eraslan, Lukas M Simon, Maria Mircea, Nikola S Mueller, Fabian J Theis. Nat Commun 2019
Gökcen Eraslan, Lukas M Simon, Maria Mircea, Nikola S Mueller, Fabian J Theis. Nat Commun 2019
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STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
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TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis.
Zhicheng Ji, Hongkai Ji. Nucleic Acids Res 2016
Zhicheng Ji, Hongkai Ji. Nucleic Acids Res 2016
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Spatial reconstruction of single-cell gene expression data.
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
Rahul Satija, Jeffrey A Farrell, David Gennert, Alexander F Schier, Aviv Regev. Nat Biotechnol 2015
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Splatter: simulation of single-cell RNA sequencing data.
Luke Zappia, Belinda Phipson, Alicia Oshlack. Genome Biol 2017
Luke Zappia, Belinda Phipson, Alicia Oshlack. Genome Biol 2017
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A statistical approach for identifying differential distributions in single-cell RNA-seq experiments.
Keegan D Korthauer, Li-Fang Chu, Michael A Newton, Yuan Li, James Thomson, Ron Stewart, Christina Kendziorski. Genome Biol 2016
Keegan D Korthauer, Li-Fang Chu, Michael A Newton, Yuan Li, James Thomson, Ron Stewart, Christina Kendziorski. Genome Biol 2016
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DrImpute: imputing dropout events in single cell RNA sequencing data.
Wuming Gong, Il-Youp Kwak, Pruthvi Pota, Naoko Koyano-Nakagawa, Daniel J Garry. BMC Bioinformatics 2018
Wuming Gong, Il-Youp Kwak, Pruthvi Pota, Naoko Koyano-Nakagawa, Daniel J Garry. BMC Bioinformatics 2018
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Dimensionality reduction for visualizing single-cell data using UMAP.
Etienne Becht, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel W H Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell. Nat Biotechnol 2018
Etienne Becht, Leland McInnes, John Healy, Charles-Antoine Dutertre, Immanuel W H Kwok, Lai Guan Ng, Florent Ginhoux, Evan W Newell. Nat Biotechnol 2018
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Full-length RNA-seq from single cells using Smart-seq2.
Simone Picelli, Omid R Faridani, Asa K Björklund, Gösta Winberg, Sven Sagasser, Rickard Sandberg. Nat Protoc 2014
Simone Picelli, Omid R Faridani, Asa K Björklund, Gösta Winberg, Sven Sagasser, Rickard Sandberg. Nat Protoc 2014
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BASiCS: Bayesian Analysis of Single-Cell Sequencing Data.
Catalina A Vallejos, John C Marioni, Sylvia Richardson. PLoS Comput Biol 2015
Catalina A Vallejos, John C Marioni, Sylvia Richardson. PLoS Comput Biol 2015
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Quantitative single-cell RNA-seq with unique molecular identifiers.
Saiful Islam, Amit Zeisel, Simon Joost, Gioele La Manno, Pawel Zajac, Maria Kasper, Peter Lönnerberg, Sten Linnarsson. Nat Methods 2014
Saiful Islam, Amit Zeisel, Simon Joost, Gioele La Manno, Pawel Zajac, Maria Kasper, Peter Lönnerberg, Sten Linnarsson. Nat Methods 2014
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Smart-seq2 for sensitive full-length transcriptome profiling in single cells.
Simone Picelli, Åsa K Björklund, Omid R Faridani, Sven Sagasser, Gösta Winberg, Rickard Sandberg. Nat Methods 2013
Simone Picelli, Åsa K Björklund, Omid R Faridani, Sven Sagasser, Gösta Winberg, Rickard Sandberg. Nat Methods 2013
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Simultaneous epitope and transcriptome measurement in single cells.
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert. Nat Methods 2017
Marlon Stoeckius, Christoph Hafemeister, William Stephenson, Brian Houck-Loomis, Pratip K Chattopadhyay, Harold Swerdlow, Rahul Satija, Peter Smibert. Nat Methods 2017
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Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics.
Kelly Street, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit. BMC Genomics 2018
Kelly Street, Davide Risso, Russell B Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, Sandrine Dudoit. BMC Genomics 2018
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scmap: projection of single-cell RNA-seq data across data sets.
Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg. Nat Methods 2018
Vladimir Yu Kiselev, Andrew Yiu, Martin Hemberg. Nat Methods 2018
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CIDR: Ultrafast and accurate clustering through imputation for single-cell RNA-seq data.
Peijie Lin, Michael Troup, Joshua W K Ho. Genome Biol 2017
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Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.
Florian Buettner, Kedar N Natarajan, F Paolo Casale, Valentina Proserpio, Antonio Scialdone, Fabian J Theis, Sarah A Teichmann, John C Marioni, Oliver Stegle. Nat Biotechnol 2015
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